I just have a question about writing the oligo file.
For my MiSeq run, a dual indexing system was used (two indices (or barcodes) per sample), one index in one adapter and one in the other: index i5 and index i7.
How should these be written in the oligo file? Will this work:
barcode TAAGGCGA-TAGATCGC APM_C01_FOP_2014_001
barcode TAAGGCGA-CTCTCTAT APM_C01_FOP_2014_002
barcode TAAGGCGA-TATCCTCT APM_C01_FOP_2014_003
Many thanks for any suggestions,